8HY6

Crystal structure of B1 NDM-1 MBL in complex with 2-amino-5-phenethylthiazole-4-carboxylic acid

PDB DOI: https://doi.org/10.2210/pdb8HY6/pdb

Classification: HYDROLASE
Organism(s): Klebsiella pneumoniae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-01-05 Released: 2023-11-01
Deposition Author(s): Yan, Y.-H., Zhu, K.-R., Li, G.-B.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.164
R-Value Work: 0.142
R-Value Observed: 0.143

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Discovery of 2-Aminothiazole-4-carboxylic Acids as Broad-Spectrum Metallo-beta-lactamase Inhibitors by Mimicking Carbapenem Hydrolysate Binding.

Yan, Y.H., Zhang, T.T., Li, R., Wang, S.Y., Wei, L.L., Wang, X.Y., Zhu, K.R., Li, S.R., Liang, G.Q., Yang, Z.B., Yang, L.L., Qin, S., Li, G.B.

(2023) J Med Chem 66: 13746-13767

PubMed: 37791640 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.3c01189
Primary Citation of Related Structures:
8HX5, 8HXE, 8HXI, 8HXN, 8HXO, 8HXP, 8HXU, 8HXV, 8HXW, 8HY1, 8HY2, 8HY6, 8HYD, 8JAO

PubMed Abstract:
Metallo-β-lactamases (MBLs) are zinc-dependent enzymes capable of hydrolyzing all bicyclic β-lactam antibiotics, posing a great threat to public health. However, there are currently no clinically approved MBL inhibitors. Despite variations in their active sites, MBLs share a common catalytic mechanism with carbapenems, forming similar reaction species and hydrolysates. We here report the development of 2-aminothiazole-4-carboxylic acids (AtCs) as broad-spectrum MBL inhibitors by mimicking the anchor pharmacophore features of carbapenem hydrolysate binding. Several AtCs manifested potent activity against B1, B2, and B3 MBLs. Crystallographic analyses revealed a common binding mode of AtCs with B1, B2, and B3 MBLs, resembling binding observed in the MBL-carbapenem product complexes. AtCs restored Meropenem activity against MBL-producing isolates. In the murine sepsis model, AtCs exhibited favorable synergistic efficacy with Meropenem, along with acceptable pharmacokinetics and safety profiles. This work offers promising lead compounds and a structural basis for the development of potential drug candidates to combat MBL-mediated antimicrobial resistance.

Organizational Affiliation

Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China.

Macromolecule Content

Total Structure Weight: 52.28 kDa
Atom Count: 4,143
Modelled Residue Count: 482
Deposited Residue Count: 482
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metallo-beta-lactamase type 2	A, B	241	Klebsiella pneumoniae	Mutation(s): 0 Gene Names: blaNDM-1 EC: 3.5.2.6
UniProt
Find proteins for C7C422 (Klebsiella pneumoniae) Explore C7C422 Go to UniProtKB: C7C422
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C7C422
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5ZX (Subject of Investigation/LOI) Query on 5ZX Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B]	E [auth A], K [auth B]	2-azanyl-5-(2-phenylethyl)-1,3-thiazole-4-carboxylic acid C₁₂ H₁₂ N₂ O₂ S JARXXMAFINZHLY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain K [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B]	F [auth A], G [auth A], H [auth A], L [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B]	C [auth A], D [auth A], I [auth B], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain I [auth B] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.164
R-Value Work: 0.142
R-Value Observed: 0.143
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.313	α = 90
b = 79.301	β = 90
c = 133.698	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
PHASER	phasing
HKL-3000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-11-01

Deposition Author(s):

Yan, Y.-H.

Zhu, K.-R.

Li, G.-B.

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81874291
National Natural Science Foundation of China (NSFC)	China	82122065
National Natural Science Foundation of China (NSFC)	China	82073698